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Author SHA1 Message Date
Nicolas Graves
293c68927f
gnu: python2-pycparser: Move to (gnu packages pypy). 
* gnu/packages/python-xyz.scm (python2-pycparser): Move from here…
* gnu/packages/pypy.scm (python2-pycparser): …to here.

Change-Id: I368e7fc7c07dcba675c1f7524e7f68145252cf73
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:58 +01:00
Nicolas Graves
15ce7c480a
gnu: python2-cffi: Move to (gnu packages pypy). 
* gnu/packages/libffi.scm (python2-cffi): Move from here…
* gnu/packages/pypy.scm (python2-cffi): …to here.

Change-Id: Ib472d2187a118c1dfec62ea9285d48fe63438fbf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:58 +01:00
Nicolas Graves
84fbf59c47
gnu: python2-cffi: Migrate to pyproject and decouple. 
Rationale: Decoupling helps us moving the package, and not worry about
inheriting package updates.

* gnu/packages/python-xyz.scm (python2-cffi)
[inherit]: Drop it.
[source]: Decrease version to 1.15.1, which is the last supported
version for Python2. The former build fails with 1.17.0.
[build-system, arguments]: Migrate to pyproject-build-system.
[name, home-page, synopsis, description, license]: Set them
explicitely.

Change-Id: Iea81e4fd3896da044a97043e2d80f5f43b28f50e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:58 +01:00
Nicolas Graves
f837d983a8
gnu: python2-pycparser: Migrate to pyproject and decouple. 
Rationale: Decoupling helps us moving the package, and not worry about
inheriting package updates.

* gnu/packages/python-xyz.scm (python2-pycparser)
[inherit]: Drop it.
[build-system, arguments]: Migrate to pyproject-build-system.
[name, home-page, synopsis, description, license]: Set them
explicitely.
[native-inputs]: Add python-setuptools.

Change-Id: Ie55f1fdc60d80ec921acabced218ec758a650cf1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:58 +01:00
Nicolas Graves
8a156ad99c
build-system: python: Accept pyproject package-with-explicit-python. 
* guix/build-system/python.scm (package-with-explicit-python): Accept
pyproject-build-system resolved lazily.

Change-Id: I6e4186b8a7d2ec17afbf6af7d0f9e709cc55e14b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:58 +01:00
Nicolas Graves
bf7bea493b
gnu: duplicity: Remove python-lockfile propagated-input. 
* gnu/packages/backup.scm (duplicity)[propagated-input]: Remove
python-lockfile.

Change-Id: Ieaa7330354c96aee0ee4c754419b10380f24acda
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:58 +01:00
Nicolas Graves
88ac4f61e5
gnu: python-cachecontrol: Remove python-lockfile propagated-input. 
* gnu/packages/python-web.scm (python-cachecontrol)[propagated-input]:
Remove python-lockfile.

Change-Id: I9801a3673d1e655148a7d9a76cb4026c26fca69d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Nicolas Graves
3aeff6c495
gnu: python-daemon: Replace python-lockfile by python-filelock. 
* gnu/packages/python-xyz.scm (python-daemon)[propagated-inputs]:
Replace python-lockfile by python-filelock.

* gnu/packages/patches/python-daemon-relax-lockfile.patch: New file
* gnu/local.mk (dist_patch_DATA): Register patch.

Change-Id: Ia12b754065a71b612b0fe626b18e2edc9d158ae7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Nicolas Graves
6863008004
gnu: python-pyvista: Ignore failing test. 
* gnu/packages/python-science.scm (python-pyvista)[arguments]
<#:test-flags>: Ignore failing test.

Change-Id: I0dba730e92c7fd7e9d7d6273bba3b5e7646278c2
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Nicolas Graves
c76d544261
gnu: python-pyts: Update to 0.13.0-0.4f3d97b. 
* gnu/packages/python-science.scm (python-pyts): Update to 0.13.0-0.4f3d97b.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-wheel.
[description]: Improve it.

Change-Id: I64947107888826ad3db8cf1e2e4d3790c6a3e070
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Nicolas Graves
9d3a8fd9b1
gnu: python-pgmpy: Ignore flaky tests. 
* gnu/packages/statistics.scm (python-pgmpy)[arguments]
<#:test-flags>: Ignore additional flaky tests.

Change-Id: I047cf08cde1d6c2157e826e80f6f93e5a9717438
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Nicolas Graves
95694c28f6
gnu: python-drep: Skip additional test. 
* gnu/packages/bioinformatics.scm (python-drep)[arguments]
<#:test-flags>: Skip additional test.
 2026-01-21 22:57:57 +01:00
Nicolas Graves
29e6768621
gnu: scregseg: Skip 'sanity-check phase. 
* gnu/packages/bioinformatics.scm (scregseg)
[arguments]<#:phases>: Skip 'sanity-check phase.
[native-inputs]: Add python-pytest.

Change-Id: If28faf66025e79210850080a18b8ce35d9ec6504
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Nicolas Graves
70c1294971
gnu: python-coolbox: Fix inputs. 
* gnu/packages/bioinformatics.scm (python-coolbox)
[native-inputs]: Remove python-pybbi.
[propagated-inputs]: Add python-pybbi.

Change-Id: Ic748f66b71b0aa489e8c0800b21cb23592f285a4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2026-01-21 22:57:57 +01:00
Sharlatan Hellseher
20c35b20c3
gnu: python-sphinx-autodoc-typehints: Update to 2.3.0. 
* gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints): Update to 2.3.0.
[arguments] <test-flags>: Rework skpped tests.
[native-inputs]: Remove nss-certs-for-test and python-nptyping.

Change-Id: Iaf7fbcf27dd4334c04acaf0efec27e0d3f140b82
 2026-01-21 22:57:57 +01:00
Sharlatan Hellseher
ce56d53c2d
gnu: Remove python-pynbody-1. 
* gnu/packages/astronomy.scm (python-pynbody-1): Delete variable.

Fixes: guix/guix#4801
Change-Id: If3461a85679cf0ff46eaeb50bcd0cc4c7eb78b16
 2026-01-21 22:57:57 +01:00
Sharlatan Hellseher
0ac053d0c0
gnu: Remove python-aioredis. 
* gnu/packages/databases.scm (python-aioredis): Delete variable.

Change-Id: If859740f6bb38fc42ae42df577d0a8c48d2af7c3
 2026-01-21 22:57:57 +01:00
Sharlatan Hellseher
ba4fd3d976
gnu: python-genomepy: Update to 0.16.3. 
* gnu/packages/bioinformatics.scm (python-genomepy): Update to 0.16.3.
[source]: Switch to git-fetch.
[native-inputs]: Remove python-pytest.

Change-Id: Iab4a30e7fb4ff31243ae0c210155a2d1896bd3cb
 2026-01-21 22:57:57 +01:00
Sharlatan Hellseher
3f5d6171f2
gnu: python-mysql-connector-python: Skip one more test. 
* gnu/packages/python-xyz.scm (python-mysql-connector-python):
[phases]{check}: Skip one more test.

Change-Id: I22277bc3cdf0634b166f3198d005c82c37b8796f
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
14ede3c201
gnu: python-timezonefinder: Use python-numpy@1. 
* gnu/packages/time.scm (python-timezonefinder):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: I2dbe7cc50b1af1453d99ac2dcfd61ffaca1aa4dd
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
d7073216e7
gnu: python-cylp: Update to 0.94.0. 
* gnu/packages/maths.scm (python-cylp): Update to 0.94.0.
[arguments] <test-flags>: Rework skipped/ignored tests.
<phases>: Add 'numpy-compatibility.'
[propagated-inputs]: Remove python-pytest.
[native-inputs]: Remove python-hypothesis, python-numpy, and
python-wheel.

Fixes: guix/guix#2912
Change-Id: Ifa466f6f0d0a1cdc3723d60a57ddeafca61dff99
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
6149a5167b
gnu: Remove music21. 
* gnu/packages/music.scm (music21): Delete variable.

Change-Id: I571e7386a543045f8aa252cad9623612bb0f8a7e
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
963313fa22
gnu: python-qutip: Update to 5.2.2. 
* gnu/packages/python-science.scm (python-qutip): Update to 5.2.2.
[arguments] <test-flags>: Rework skipped/ignored tests.
<phases>: Use default 'check; add 'remove-local-source.
[propagated-inputs]: Add python-cvxopt, python-cvxpy, python-mpi4py,
python-mpmath, and python-tqdm.
[native-inputs]: Remove python-numpy, python-packaging, python-scipy,
and python-wheel; add python-pytest-rerunfailures.

Change-Id: I1ee08658e6a7c6ef2c6b42b9d121113dedad04f7
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
41e90b9fb3
gnu: python-petrofit: Reduce closure size. 
* gnu/packages/astronomy.scm (python-petrofit):
[phases]{relax-requirements}: New phase.
[propagated-inputs]: Remove jupyter, python-cython, python-ipywidgets,
and python-pytest-astropy-header.
[native-inputs]: Remove python-pytest-xdist, python-setuptools, and
python-wheel; add python-cython and python-pytest-astropy-header.

Change-Id: Id5e79feb6f47e9b6d00568cf1ec54dc0c18fd52b
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
59d2b75e54
gnu: python-statmorph: Use python-numpy@1. 
* gnu/packages/astronomy.scm (python-statmorph):
[propagated-inputs]: Remove python-numpy, add python-numpy-1.

Change-Id: Ibe7a78c4261398867dd0413feb9101b4d79c9eeb
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
45639ee51b
gnu: python-pysat: Skip more tests. 
* gnu/packages/astronomy.scm (python-pysat):
[arguments] <test-flags>: Run tests in parallel and skip more failing
ones.
[native-inputs]: Remove python-wheel.

Change-Id: I164dfe85e34d01610b6b58407913a08a557e27fd
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
0a29f178b6
gnu: python-pyopencl: Update to 2026.1. 
* gnu/packages/opencl.scm (python-pyopencl): Update to 2026.1.
[phases]{pre-build}: New phase.
[propagated-inputs]: Remove python-mako; add python-typing-extensions.
[native-inputs]: Add pocl, python-mako, and python-pytest.
[home-page]: Fix lint warning: "permanent redirect from
https://mathema.tician.de/software/pyopencl to
https://mathema.tician.de/software/pyopencl/"

Change-Id: I08567d11ff612cdb9d08c62c6ba1928bb73f9837
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
155e793b0f
gnu: python-nanobind: Update to 2.10.2. 
* gnu/packages/python-xyz.scm (python-nanobind): Update to 2.10.2.
[native-inputs]: Add python-numpy, python-pathspec, and python-scipy.
[synopsis]: Fix lint warning: "synopsis should start with an upper-case
letter or digit".

Change-Id: I26dd624d3a9ead7af7744769cc59f05bb56de56d
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
e8ad519b19
gnu: python-pytools: Add missing propagated inputs, enable tests. 
* gnu/packages/opencl.scm (python-pytools):
[arguments] <tests?>: Enable.
[propagated-inputs]: Remove python-appdirs and python-numpy; add
python-platformdirs, python-siphash24, and python-typing-extensions.
[native-inputs]: Add python-pytest.

Change-Id: Ib4635f375306b1ea9415bd0eca79013d0521b9cc
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
f626da074d
gnu: Add python-siphash24. 
* gnu/packages/python-xyz.scm (python-siphash24): New variable.

Change-Id: I297103197b867e9be3a60caf53a8536f5c32aa63
 2026-01-21 22:57:56 +01:00
Sharlatan Hellseher
578661549f
gnu: Add c-siphash. 
* gnu/packages/c.scm (c-siphash): New variable.

Change-Id: Icc2cbe8cb408ea345d3921b4fce74e5761f79b87
 2026-01-21 22:57:55 +01:00
Sharlatan Hellseher
0cf11223f6
gnu: Add c-stdaux. 
* gnu/packages/c.scm (c-stdaux): New variable.

Change-Id: Iddb4f0f77e5b4c9be03d8029272d47e2dddf7bf1
 2026-01-21 22:57:52 +01:00
Sharlatan Hellseher
85cd716156
gnu: python-pymol: Use python-numpy@1. 
* gnu/packages/chemistry.scm (python-pymol):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.

Change-Id: Icfb0eb4116ecb7b9d34fe13bc8bd81d85a4a64ec
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
09ce0dde5b
gnu: openmm: Remove shaky tests. 
The package could not finish build in CI because of some not
deterministic tests, see:
<https://ci.guix.gnu.org/build/16867177/details>. This change removes
some of them.

* gnu/packages/machine-learning.scm (openmm):
[phases]{remove-shaky-tests}: New phase.

Change-Id: I508b23db8b6f0d5a567561b190897bc90cb8faf3
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
e0f28a000f
gnu: python-pymc: Update to 5.27.0. 
* gnu/packages/statistics.scm (python-pymc): Update to 5.27.0.
[arguments] <phases>: Remove 'relax-requirements.

Change-Id: I8e7cb8d2a035b922c998e79b7a07f55fe41b9979
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
6d630e6b06
gnu: python-pytensor: Update to 2.36.3. 
* gnu/packages/python-science.scm (python-pytensor): Update to 2.36.3.
[arguments] <test-flags>: Add option to skip/disable benchmark tests and
rework skipped tests.
[native-inputs]: Add python-pytest-benchmark and python-pytest-xdist.

Change-Id: I9c3c42c21091524741ccef55e4698b59e818512d
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
b554be84d1
gnu: python-fastparquet: Update to 2025.12.0. 
* gnu/packages/databases.scm (python-fastparquet): Update to 2025.12.0.
[arguments] <phases>: Remove 'relax-requirements,'pretend-version, and
'build-cython-extensions; add 'remove-dependencies-on-git, 'set-version
and 'remove-local-source.
[native-inputs]: Remove python-wheel.

Change-Id: I808357310fbd78c1465d638788a3040ba2b8a452
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
a9f599705f
gnu: python-pygam: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (python-pygam): Update to 0.12.0.
[arguments] <test-flags>: Skip one test.
<phases>: Remove 'patch-pyproject.
[propagated-inputs]: Remove python-black, python-flake8, python-ipython,
and python-poetry-core.
[native-inputs]: Remove python-pytest-cov; add python-matplotlib and
python-setuptools.

Change-Id: I5b3b95deb2bbe455582d4c74fe672c62b9aa8ff4
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
3b7e8b5d27
gnu: python-pyemd: Use python-numpy@1. 
* gnu/packages/python-xyz.scm (python-pyemd):
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: I7cad3d609f1eec432d3e77945ffd2b2dc30b4900
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
775282cea6
gnu: python-pot: Update to 0.9.6.post1. 
* gnu/packages/machine-learning.scm (python-pot): Update to 0.9.6.post1.
[arguments]: Drop all.
[propagated-inputs]: Add python-cvxopt and python-matplotlib.
[native-inputs]: Remove python-pytest-cov.

Change-Id: I763bf521a30f1bd4067089133421239af160173c
 2026-01-21 22:57:04 +01:00
Sharlatan Hellseher
a4dfc97b06
gnu: python-pingouin: Fix tests. 
* gnu/packages/python-science.scm (python-pingouin):
[arguments] <test-flags>: Rework skipped tests.
<phases>: Add 'relax-requirements.
[native-inputs]: Remove python-pytest-cov; add python-setuptools.

Change-Id: If45e91fabbd479819731041c09dd6e1e561774d6
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
4e12abfc60
gnu: python-phenograph: Fix tests. 
* gnu/packages/bioinformatics.scm (python-phenograph):
[arguments] <test-flags>: Skip 3 more tests.
<phases>: Remove 'disable-leiden-test, and move logic to <#:test-flags>.
[propagated-inputs]: Remove python-numpy; add python-numpy-1.
[native-inputs]: Remove python-wheel.

Change-Id: Id7a7cb67adb13749bde59ad93d5c1125f2903065
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
5e2daaf995
gnu: python-scikit-survival: Fix indentation. 
* gnu/packages/python-science.scm (python-scikit-survival): Fix indentation.

Change-Id: Iff0ab38a0b484938613df08ffb0fbd83da489289
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
2346df813e
gnu: python-scikit-survival: Update to 0.26.0. 
* gnu/packages/python-science.scm (python-scikit-survival): Update to 0.26.0.
[native-inputs]: Add python-pytest-xdist.

Change-Id: If92ba627c894cb65976b7687062e738656b06e96
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
0230ecdbad
gnu: Remove python-dask-expr. 
* gnu/packages/python-science.scm (python-dask/bootstrap)
(python-dask-expr): Delete variables.

Fixes: guix/guix#4766
Change-Id: I8243329353fe41b0ffff35fd4383a9a09047cd52
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
d9d182120d
gnu: openmm: Update to 8.4.0. 
* gnu/packages/machine-learning.scm (openmm): Update to 8.4.0.

Change-Id: If91f5557966b7982b3504800d7761cc9b79b3af2
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
09274fbc5c
gnu: Remove fanc. 
* gnu/packages/bioinformatics.scm (fanc): Delete variable.

Change-Id: I6ecb68155c021a67ff548bb2bd3bb6052676dc3a
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
2703fec25e
gnu: Remove ginga-qt5. 
* gnu/packages/astronomy.scm (ginga-qt5): Delete variable.

Change-Id: I86a926bd8af1a999780c64e4bd435238d7dd3c85
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
85cfa28f4b
gnu: Remove python-webbpsf. 
* gnu/packages/astronomy.scm (python-webbpsf): Delete variable.

Change-Id: I87374a9f04ad87eb940a9ad2751a217f779e5ea3
 2026-01-21 22:57:03 +01:00
Sharlatan Hellseher
86f6f29dfd
gnu: Remove python-watchgod. 
* gnu/packages/python-xyz.scm (python-watchgod): Delete variable.

Change-Id: I52cbd0577de38bb21094ed8f6ee5ef14741634e0
 2026-01-21 22:57:03 +01:00